OpenRaiser/Intern-Atlas huggingface dataset:
Clinical Concept Extraction: a Methodology Review
Venue: arXiv cs.IR 2020
Year: 2020

Background Concept extraction, a subdomain of natural language processing (NLP) with a focus on extracting concepts of interest, has been adopted to computationally extract clinical information from text for a wide range of applications ranging from clinical decision support to care quality improvement. Objectives In this literature review, we provide a methodology review of clinical concept extraction, aiming to catalog development processes, available methods and tools, and specific considerations when developing clinical concept extraction applications. Methods Based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, a literature search was conducted for retrieving EHR-based information extraction articles written in English and published from January 2009 through June 2019 from Ovid MEDLINE In-Process & Other Non-Indexed Citations, Ovid MEDLINE, Ovid EMBASE, Scopus, Web of Science, and the ACM Digital Library. Results A total of 6,686 publications were retrieved. After title and abstract screening, 228 publications were selected. The methods used for developing clinical concept extraction applications were discussed in this review.
Manipulating Node Similarity Measures in Networks
Venue: arXiv cs.SI 2020
Year: 2020

Node similarity measures quantify how similar a pair of nodes are in a network. These similarity measures turn out to be an important fundamental tool for many real world applications such as link prediction in networks, recommender systems etc. An important class of similarity measures are local similarity measures. Two nodes are considered similar under local similarity measures if they have large overlap between their neighboring set of nodes. Manipulating node similarity measures via removing edges is an important problem. This type of manipulation, for example, hinders effectiveness of link prediction in terrorists networks. Fortunately, all the popular computational problems formulated around manipulating similarity measures turn out to be NP-hard. We, in this paper, provide fine grained complexity results of these problems through the lens of parameterized complexity. In particular, we show that some of these problems are fixed parameter tractable (FPT) with respect to various natural parameters whereas other problems remain intractable W[1]-hard and W[2]-hard in particular). Finally we show the effectiveness of our proposed FPT algorithms on real world datasets as well as synthetic networks generated using Barabasi-Albert and Erdos-Renyi models.
Evaluation of Sentence Representations in Polish
Venue: arXiv cs.CL 2020
Year: 2020

Methods for learning sentence representations have been actively developed in recent years. However, the lack of pre-trained models and datasets annotated at the sentence level has been a problem for low-resource languages such as Polish which led to less interest in applying these methods to language-specific tasks. In this study, we introduce two new Polish datasets for evaluating sentence embeddings and provide a comprehensive evaluation of eight sentence representation methods including Polish and multilingual models. We consider classic word embedding models, recently developed contextual embeddings and multilingual sentence encoders, showing strengths and weaknesses of specific approaches. We also examine different methods of aggregating word vectors into a single sentence vector.
Learning Boolean Circuits with Neural Networks
Venue: arXiv cs.LG 2020
Year: 2020

While on some natural distributions, neural-networks are trained efficiently using gradient-based algorithms, it is known that learning them is computationally hard in the worst-case. To separate hard from easy to learn distributions, we observe the property of local correlation: correlation between local patterns of the input and the target label. We focus on learning deep neural-networks using a gradient-based algorithm, when the target function is a tree-structured Boolean circuit. We show that in this case, the existence of correlation between the gates of the circuit and the target label determines whether the optimization succeeds or fails. Using this result, we show that neural-networks can learn the (log n)-parity problem for most product distributions. These results hint that local correlation may play an important role in separating easy/hard to learn distributions. We also obtain a novel depth separation result, in which we show that a shallow network cannot express some functions, while there exists an efficient gradient-based algorithm that can learn the very same functions using a deep network. The negative expressivity result for shallow networks is obtained by a reduction from results in communication complexity, that may be of independent interest.
PREMA: Principled Tensor Data Recovery from Multiple Aggregated Views
Venue: arXiv cs.LG 2020
Year: 2020

Multidimensional data have become ubiquitous and are frequently encountered in situations where the information is aggregated over multiple data atoms. The aggregation can be over time or other features, such as geographical location. We often have access to multiple aggregated views of the same data, each aggregated in one or more dimensions, especially when data are collected or measured by different agencies. For instance, item sales can be aggregated temporally, and over groups of stores based on their location or affiliation. However, data mining and machine learning models benefit from detailed data for personalized analysis and prediction. Thus, data disaggregation algorithms are becoming increasingly important in various domains. The goal of this paper is to reconstruct finer-scale data from multiple coarse views, aggregated over different (subsets of) dimensions. The proposed method, called PREMA, leverages low-rank tensor factorization tools to fuse the multiple views and provide recovery guarantees under certain conditions. PREMA can tackle challenging scenarios, such as missing or partially observed data, double aggregation, and even blind disaggregation (without knowledge of the aggregation patterns) using a variant of PREMA called B-PREMA. To showcase the effectiveness of PREMA, the paper includes extensive experiments using real data from different domains: retail sales, crime counts, and weather observations.
Spatially Coupled LDPC Codes with Sub-Block Locality
Venue: arXiv cs.IT 2020
Year: 2020

A new type of spatially coupled low-density parity-check (SC-LDPC) codes motivated by practical storage applications is presented. SC-LDPCL codes (suffix 'L' stands for locality) can be decoded locally at the level of sub-blocks that are much smaller than the full code block, thus offering flexible access to the coded information alongside the strong reliability of the global full-block decoding. Toward that, we propose constructions of SC-LDPCL codes that allow controlling the trade-off between local and global correction performance. In addition to local and global decoding, the paper develops a density-evolution analysis for a decoding mode we call semi-global decoding, in which the decoder has access to the requested sub-block plus a prescribed number of sub-blocks around it. SC-LDPCL codes are also studied under a channel model with variability across sub-blocks, for which decoding-performance lower bounds are derived.
Induced Inflection-Set Keyword Search in Speech
Venue: arXiv cs.CL 2020
Year: 2020

We investigate the problem of searching for a lexeme-set in speech by searching for its inflectional variants. Experimental results indicate how lexeme-set search performance changes with the number of hypothesized inflections, while ablation experiments highlight the relative importance of different components in the lexeme-set search pipeline and the value of using curated inflectional paradigms. We provide a recipe and evaluation set for the community to use as an extrinsic measure of the performance of inflection generation approaches.
Sage: Parallel Semi-Asymmetric Graph Algorithms for NVRAMs
Venue: arXiv cs.DC 2020
Year: 2020

Non-volatile main memory (NVRAM) technologies provide an attractive set of features for large-scale graph analytics, including byte-addressability, low idle power, and improved memory-density. NVRAM systems today have an order of magnitude more NVRAM than traditional memory (DRAM). NVRAM systems could therefore potentially allow very large graph problems to be solved on a single machine, at a modest cost. However, a significant challenge in achieving high performance is in accounting for the fact that NVRAM writes can be much more expensive than NVRAM reads. In this paper, we propose an approach to parallel graph analytics using the Parallel Semi-Asymmetric Model (PSAM), in which the graph is stored as a read-only data structure (in NVRAM), and the amount of mutable memory is kept proportional to the number of vertices. Similar to the popular semi-external and semi-streaming models for graph analytics, the PSAM approach assumes that the vertices of the graph fit in a fast read-write memory (DRAM), but the edges do not. In NVRAM systems, our approach eliminates writes to the NVRAM, among other benefits. To experimentally study this new setting, we develop Sage, a parallel semi-asymmetric graph engine with which we implement provably-efficient (and often work-optimal) PSAM algorithms for over a dozen fundamental graph problems. We experimentally study Sage using a 48-core machine on the largest publicly-available real-world graph (the Hyperlink Web graph with over 3.5 billion vertices and 128 billion edges) equipped with Optane DC Persistent Memory, and show that Sage outperforms the fastest prior systems designed for NVRAM. Importantly, we also show that Sage nearly matches the fastest prior systems running solely in DRAM, by effectively hiding the costs of repeatedly accessing NVRAM versus DRAM.
Variable Selection with Copula Entropy
Venue: arXiv cs.LG 2020
Year: 2020

Variable selection is of significant importance for classification and regression tasks in machine learning and statistical applications where both predictability and explainability are needed. In this paper, a Copula Entropy (CE) based method for variable selection which use CE based ranks to select variables is proposed. The method is both model-free and tuning-free. Comparison experiments between the proposed method and traditional variable selection methods, such as Distance Correlation, Hilbert-Schmidt Independence Criterion, Stepwise Selection, regularized generalized linear models and Adaptive LASSO, were conducted on the UCI heart disease data. Experimental results show that CE based method can select the `right' variables out more effectively and derive better interpretable results than traditional methods do without sacrificing accuracy performance. It is believed that CE based variable selection can help to build more explainable models.
Latency and timeliness in multi-hop satellite networks
Venue: arXiv cs.IT 2020
Year: 2020

The classical definition of network delay has been recently augmented by the concept of information timeliness, or Age of Information (AoI). We analyze the network delay and the AoI in a multi-hop satellite network that relays status updates from satellite 1, receiving uplink traffic from ground devices, to satellite K, using K-2 intermediate satellite nodes. The last node, K, is the closest satellite with connectivity to a ground station. The satellite formation is modeled as a queue network of M/M/1 systems connected in series. The scenario is then generalized for the case in which all satellites receive uplink traffic from ground, and work at the same time as relays of the packets from the previous nodes. The results show that the minimum average AoI is experienced at a decreasing system utilization when the number of nodes is increased. Furthermore, unloading the first nodes of the chain reduces the queueing time and therefore the average AoI. These findings provide insights for designing multi-hop satellite networks for latency-sensitive applications.
Neural Architecture Evolution in Deep Reinforcement Learning for Continuous Control
Venue: arXiv cs.LG 2020
Year: 2020

Current Deep Reinforcement Learning algorithms still heavily rely on handcrafted neural network architectures. We propose a novel approach to automatically find strong topologies for continuous control tasks while only adding a minor overhead in terms of interactions in the environment. To achieve this, we combine Neuroevolution techniques with off-policy training and propose a novel architecture mutation operator. Experiments on five continuous control benchmarks show that the proposed Actor-Critic Neuroevolution algorithm often outperforms the strong Actor-Critic baseline and is capable of automatically finding topologies in a sample-efficient manner which would otherwise have to be found by expensive architecture search.
Federated Learning over Wireless Networks: Convergence Analysis and Resource Allocation
Venue: arXiv cs.LG 2020
Year: 2020

There is an increasing interest in a fast-growing machine learning technique called Federated Learning, in which the model training is distributed over mobile user equipments (UEs), exploiting UEs' local computation and training data. Despite its advantages in data privacy-preserving, Federated Learning (FL) still has challenges in heterogeneity across UEs' data and physical resources. We first propose a FL algorithm which can handle the heterogeneous UEs' data challenge without further assumptions except strongly convex and smooth loss functions. We provide the convergence rate characterizing the trade-off between local computation rounds of UE to update its local model and global communication rounds to update the FL global model. We then employ the proposed FL algorithm in wireless networks as a resource allocation optimization problem that captures the trade-off between the FL convergence wall clock time and energy consumption of UEs with heterogeneous computing and power resources. Even though the wireless resource allocation problem of FL is non-convex, we exploit this problem's structure to decompose it into three sub-problems and analyze their closed-form solutions as well as insights to problem design. Finally, we illustrate the theoretical analysis for the new algorithm with Tensorflow experiments and extensive numerical results for the wireless resource allocation sub-problems. The experiment results not only verify the theoretical convergence but also show that our proposed algorithm outperforms the vanilla FedAvg algorithm in terms of convergence rate and testing accuracy.
Classification Calibration for Long-tail Instance Segmentation
Venue: arXiv cs.CV 2020
Year: 2020

Remarkable progress has been made in object instance detection and segmentation in recent years. However, existing state-of-the-art methods are mostly evaluated with fairly balanced and class-limited benchmarks, such as Microsoft COCO dataset [8]. In this report, we investigate the performance drop phenomenon of state-of-the-art two-stage instance segmentation models when processing extreme long-tail training data based on the LVIS [5] dataset, and find a major cause is the inaccurate classification of object proposals. Based on this observation, we propose to calibrate the prediction of classification head to improve recognition performance for the tail classes. Without much additional cost and modification of the detection model architecture, our calibration method improves the performance of the baseline by a large margin on the tail classes. Codes will be available. Importantly, after the submission, we find significant improvement can be further achieved by modifying the calibration head, which we will update later.
Shielding Collaborative Learning: Mitigating Poisoning Attacks through Client-Side Detection
Venue: arXiv cs.CR 2020
Year: 2020

Collaborative learning allows multiple clients to train a joint model without sharing their data with each other. Each client performs training locally and then submits the model updates to a central server for aggregation. Since the server has no visibility into the process of generating the updates, collaborative learning is vulnerable to poisoning attacks where a malicious client can generate a poisoned update to introduce backdoor functionality to the joint model. The existing solutions for detecting poisoned updates, however, fail to defend against the recently proposed attacks, especially in the non-IID setting. In this paper, we present a novel defense scheme to detect anomalous updates in both IID and non-IID settings. Our key idea is to realize client-side cross-validation, where each update is evaluated over other clients' local data. The server will adjust the weights of the updates based on the evaluation results when performing aggregation. To adapt to the unbalanced distribution of data in the non-IID setting, a dynamic client allocation mechanism is designed to assign detection tasks to the most suitable clients. During the detection process, we also protect the client-level privacy to prevent malicious clients from stealing the training data of other clients, by integrating differential privacy with our design without degrading the detection performance. Our experimental evaluations on two real-world datasets show that our scheme is significantly robust to two representative poisoning attacks.
Adversarial Example in Remote Sensing Image Recognition
Venue: arXiv cs.CV 2020
Year: 2020

With the wide application of remote sensing technology in various fields, the accuracy and security requirements for remote sensing images (RSIs) recognition are also increasing. In recent years, due to the rapid development of deep learning in the field of image recognition, RSI recognition models based on deep convolution neural networks (CNNs) outperform traditional hand-craft feature techniques. However, CNNs also pose security issues when they show their capability of accurate classification. By adding a very small variation of the adversarial perturbation to the input image, the CNN model can be caused to produce erroneous results with extremely high confidence, and the modification of the image is not perceived by the human eye. This added adversarial perturbation image is called an adversarial example, which poses a serious security problem for systems based on CNN model recognition results. This paper, for the first time, analyzes adversarial example problem of RSI recognition under CNN models. In the experiments, we used different attack algorithms to fool multiple high-accuracy RSI recognition models trained on multiple RSI datasets. The results show that RSI recognition models are also vulnerable to adversarial examples, and the models with different structures trained on the same RSI dataset also have different vulnerabilities. For each RSI dataset, the number of features also affects the vulnerability of the model. Many features are good for defensive adversarial examples. Further, we find that the attacked class of RSI has an attack selectivity property. The misclassification of adversarial examples of the RSIs are related to the similarity of the original classes in the CNN feature space. In addition, adversarial examples in RSI recognition are of great significance for the security of remote sensing applications, showing a huge potential for future research.
Decomposing Collectives for Exploiting Multi-lane Communication
Venue: arXiv cs.DC 2020
Year: 2020

Many modern, high-performance systems increase the cumulated node-bandwidth by offering more than a single communication network and/or by having multiple connections to the network. Efficient algorithms and implementations for collective operations as found in, e.g., MPI must be explicitly designed for such multi-lane capabilities. We discuss a model for the design of multi-lane algorithms, and in particular give a recipe for converting any standard, one-ported, (pipelined) communication tree algorithm into a multi-lane algorithm that can effectively use $k$ lanes simultaneously. We first examine the problem from the perspective of \emph{self-consistent performance guidelines}, and give simple, \emph{full-lane, mock-up implementations} of the MPI broadcast, reduction, scan, gather, scatter, allgather, and alltoall operations using only similar operations of the given MPI library itself in such a way that multi-lane capabilities can be exploited. These implementations which rely on a decomposition of the communication domain into communicators for nodes and lanes are full-fledged and readily usable implementations of the MPI collectives. The mock-up implementations, contrary to expectation, in many cases show surprising performance improvements with different MPI libraries on a small 36-node dual-socket, dual-lane Intel OmniPath cluster, indicating severe problems with the native MPI library implementations. Our full-lane implementations are in many cases considerably more than a factor of two faster than the corresponding MPI collectives. We see similar results on the larger Vienna Scientific Cluster, VSC-3. These experiments indicate considerable room for improvement of the MPI collectives in current libraries including more efficient use of multi-lane communication.
Approximately Stable Committee Selection
Venue: arXiv cs.GT 2020
Year: 2020

In the committee selection problem, we are given $m$ candidates, and $n$ voters. Candidates can have different weights. A committee is a subset of candidates, and its weight is the sum of weights of its candidates. Each voter expresses an ordinal ranking over all possible committees. The only assumption we make on preferences is monotonicity: If $S \subseteq S'$ are two committees, then any voter weakly prefers $S'$ to $S$. We study a general notion of group fairness via stability: A committee of given total weight $K$ is stable if no coalition of voters can deviate and choose a committee of proportional weight, so that all these voters strictly prefer the new committee to the existing one. Extending this notion to approximation, for parameter $c \ge 1$, a committee $S$ of weight $K$ is said to be $c$-approximately stable if for any other committee $S'$ of weight $K'$, the fraction of voters that strictly prefer $S'$ to $S$ is strictly less than $\frac{c K'}{K}$. When $c = 1$, this condition is equivalent to classical core stability. The question we ask is: Does a $c$-approximately stable committee of weight at most any given value $K$ always exist for constant $c$? It is relatively easy to show that there exist monotone preferences for which $c \ge 2$. However, even for simple and widely studied preference structures, a non-trivial upper bound on $c$ has been elusive. In this paper, we show that $c = O(1)$ for all monotone preference structures. Our proof proceeds via showing an existence result for a randomized notion of stability, and iteratively rounding the resulting fractional solution.